I am trying to install the R library BRugs on my Ubuntu 12.04 desktop.
> sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: x86_64-pc-linux-gnu (64-bit)
But I get the following error:
* installing *source* package ‘BRugs’ ...
** package ‘BRugs’ successfully unpacked and MD5 sums checked
checking for prefix by checking for OpenBUGS... /usr/bin/OpenBUGS
checking for gcc... gcc
checking whether the C compiler works... no
configure: error: in `/tmp/RtmpnNLTG1/R.INSTALL488b7635d4c0/BRugs':
configure: error: C compiler cannot create executables
See `config.log' for more details
ERROR: configuration failed for package ‘BRugs’
* removing ‘/home/myuser/lib/R/BRugs’
Warning in install.packages("BRugs") :
installation of package ‘BRugs’ had non-zero exit status
The downloaded source packages are in
‘/tmp/Rtmp2ytOWn/downloaded_packages’
Here is a link to config.log. It is difficult to tell what the error is, except that the errors starts with gcc: error: unrecognized option '-V'.
How can I get around this error (and install BRugs)?
According to the package description:
Versions running on Linux and on 64-bit R under Windows are in "beta"
status and less efficient.
And it looks like configure is trying to build the package using 32-bit executables (note the -m32 flags). It's probably best if you contact the package maintainer(s) and ask them how to build the 32-bit executable under 64-bit Ubuntu.
Related
I am trying to install Tensorflow Lite on Raspberry Pi Zero W. I followed the steps from the official website (https://www.tensorflow.org/lite/guide/build_cmake_arm). But I get the following error message:
-- The C compiler identification is unknown
-- The CXX compiler identification is unknown
-- Check for working C compiler: /home/pi/toolchains/arm-rpi-linux-gnueabihf/x64-gcc-6.5.0/arm-rpi-linux-gnueabihf/bin/arm-rpi-linux-gnueabihf-gcc
-- Check for working C compiler: /home/pi/toolchains/arm-rpi-linux-gnueabihf/x64-gcc-6.5.0/arm-rpi-linux-gnueabihf/bin/arm-rpi-linux-gnueabihf-gcc -- broken
CMake Error at /usr/share/cmake-3.16/Modules/CMakeTestCCompiler.cmake:60 (message):
The C compiler
"/home/pi/toolchains/arm-rpi-linux-gnueabihf/x64-gcc-6.5.0/arm-rpi-linux-gnueabihf/bin/arm-rpi-linux-gnueabihf-gcc"
is not able to compile a simple test program.
It fails with the following output:
Change Dir: /home/pi/Project/cmake-3.16.0/CMakeFiles/CMakeTmp
Run Build Command(s):/usr/bin/make cmTC_ed1a3/fast && /usr/bin/make -f CMakeFiles/cmTC_ed1a3.dir/build.make CMakeFiles/cmTC_ed1a3.dir/build
make[1]: Entering directory '/home/pi/Project/cmake-3.16.0/CMakeFiles/CMakeTmp'
Building C object CMakeFiles/cmTC_ed1a3.dir/testCCompiler.c.o
/home/pi/toolchains/arm-rpi-linux-gnueabihf/x64-gcc-6.5.0/arm-rpi-linux-gnueabihf/bin/arm-rpi-linux-gnueabihf-gcc -march=armv6 -mfpu=vfp -funsafe-math-optimizations -o CMakeFiles/cmTC_ed1a3.dir/testCCompiler.c.o -c /home/pi/Project/cmake-3.16.0/CMakeFiles/CMakeTmp/testCCompiler.c
/home/pi/toolchains/arm-rpi-linux-gnueabihf/x64-gcc-6.5.0/arm-rpi-linux-gnueabihf/bin/arm-rpi-linux-gnueabihf-gcc: 1: /home/pi/toolchains/arm-rpi-linux-gnueabihf/x64-gcc-6.5.0/arm-rpi-linux-gnueabihf/bin/arm-rpi-linux-gnueabihf-gcc: Syntax error: ")" unexpected
make[1]: *** [CMakeFiles/cmTC_ed1a3.dir/build.make:66: CMakeFiles/cmTC_ed1a3.dir/testCCompiler.c.o] Error 2
make[1]: Leaving directory '/home/pi/Project/cmake-3.16.0/CMakeFiles/CMakeTmp'
make: *** [Makefile:121: cmTC_ed1a3/fast] Error 2
CMake will not be able to correctly generate this project.
Call Stack (most recent call first):
CMakeLists.txt:44 (project)
Configuring incomplete, errors occurred!
See also "/home/pi/Project/cmake-3.16.0/CMakeFiles/CMakeOutput.log".
See also "/home/pi/Project/cmake-3.16.0/CMakeFiles/CMakeError.log".
Does anyone know how to fix the problem?
I ran into the same problem like you!
The instructions given at https://www.tensorflow.org/lite/guide/build_cmake_arm?hl=en are not intended to be executed on the Raspberry Pi (at least the last ones).
Let me share, what I'll figured out.
Short answer:
you're trying to run a cross-compile of TensorFlow Lite for an ARM made for x86 platform on an ARM system (your Raspberry Pi). What you're trying to do actually needs to be done on an x86 platform.
(on the top of the tutorial page is a hint: "following instructions have been tested on Ubuntu 16.04.3 64-bit PC (AMD64)" which reveals that the commands have been run on x86)
Some details:
The message ‘Syntax error: "(" unexpected’ probably comes from a shell. Why is a shell trying to execute your binary? Because the kernel tried and gave up. Why did the kernel fail to run the program? Because the executable is not in a supported format -> meant to be run on x86 but was executed on ARM.
https://unix.stackexchange.com/questions/336436/syntax-error-unexpected-when-execute-a-compiled-c-program
With older TensorFlow versions it was possible to compile TF lite on the Raspberry Pi itself via the
./tensorflow-2.4.1/tensorflow/lite/tools/make/download_dependencies.sh /and build_aarch64_lib.sh scripts.
However, this scripts got removed in version 2.8 (or even with an earlier version before). See note in the Readme of the Git: https://github.com/tensorflow/tensorflow/blob/master/tensorflow/lite/tools/make/README.md
Using Python for inference
Unfortunately I have no real solution how to compile / built TensorFlow Lite on the Raspberry itself. I personally ended up using Python (only needed inference) and followed this Tutorial:
https://qengineering.eu/install-tensorflow-2.7-on-raspberry-64-os.html
I get the following error:
* installing *source* package ‘lwgeom’ ...
** package ‘lwgeom’ successfully unpacked and MD5 sums checked
** using staged installation
configure: CC: gcc -std=gnu99
configure: CXX: g++ -std=gnu++11
configure: pkg-config proj exists, will use it
checking proj_api.h usability... no
checking proj_api.h presence... no
checking for proj_api.h... no
configure: error: proj_api.h not found in standard or given locations.
ERROR: configuration failed for package ‘lwgeom’
Previously I have follow this: https://philmikejones.me/tutorials/2018-08-29-install-sf-ubuntu/
sf and rgdal are installed without problem
I have other three machines with the same OS and have not encounter this issue before.
R version:
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
I was looking for the exact same issue and I found a solution:
devtools::install_github("r-spatial/lwgeom")
For reasons I can't comprehend, it seems that CRAN version doesn't get along with Ubuntu, but installing it via devtools allowed me to install lwgeom first and then tmaptools with no trouble at all. I hope it helps!
I cannot install Xdebug on Homestead because I get some sort of compile error.
I am following the Xdebug Wizard (https://xdebug.org/wizard) and when I input the ./configure command I get this error:
configure: error: in /home/vagrant/code/xdebug-2.7.2:
configure: error: cannot run C compiled programs.
If you meant to cross compile, use '--host'.
See 'config.log' for more details
This points at that you don't have a C compiler installed at all. You will have better luck after installing the php-dev package first, which should pull in the compilers that PHP extensions will need.
I'm trying to upgrade my Vim to MacVim by running:
$ brew install macvim --with--override-system-vim
I'm getting this error message saying that the package cannot be compiled:
configure: creating cache auto/config.cache
checking whether make sets $(MAKE)... yes
checking for gcc... clang
checking whether the C compiler works... no
configure: error: in `/private/tmp/macvim-20161028-10122-1pp1odr/macvim-snapshot-113/src':
configure: error: C compiler cannot create executables
See `config.log' for more details
I have Xcode 8.1 installed on my machine. But brew seems to think it's a pre-release version:
Warning: You are using a pre-release version of Xcode.
You may encounter build failures or other breakages.
Please create pull-requests instead of filing issues.
Not sure if this is the correct place for this kind of question. If not, please point me in the right direction.
I'm using OSX 10.5.8 on a white 13" macbook with Xcode 3.1.4. When installing py27-bottleneck through macports, I get the following error
---> Building py27-bottleneck
running build
running build_py
package init file 'bottleneck/tests/__init__.py' not found (or not a regular file)
package init file 'bottleneck/src/func/__init__.py' not found (or not a regular file)
package init file 'bottleneck/src/move/__init__.py' not found (or not a regular file)
package init file 'bottleneck/tests/__init__.py' not found (or not a regular file)
package init file 'bottleneck/src/func/__init__.py' not found (or not a regular file)
package init file 'bottleneck/src/move/__init__.py' not found (or not a regular file)
running build_ext
building 'func' extension
/usr/bin/gcc-4.2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -arch i386 -I/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/include -I/opt/local/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c bottleneck/src/func/func.c -o build/temp.macosx-10.5-i386-2.7/bottleneck/src/func/func.o
In file included from /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1760,
from /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17,
from /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
from bottleneck/src/func/func.c:314:
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION"
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/include/numpy/__ufunc_api.h:242: warning: ?_import_umath? defined but not used
cc1(53864) malloc: *** mmap(size=298745856) failed (error code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
cc1: out of memory allocating 298742336 bytes after a total of 0 bytes
error: command '/usr/bin/gcc-4.2' failed with exit status 1
Command failed: cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_python_py-bottleneck/py27-bottleneck/work/Bottleneck-0.8.0" && /opt/local/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7 setup.py --no-user-cfg build
Exit code: 1
Error: org.macports.build for port py27-bottleneck returned: command execution failed
Warning: targets not executed for py27-bottleneck: org.macports.activate org.macports.build org.macports.destroot org.macports.install
Please see the log file for port py27-bottleneck for details:
/opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_ports_python_py-bottleneck/py27-bottleneck/main.log
Error: Problem while installing py27-bottleneck
I don't really know what the problem is and why this had happened, but what I noticed was that macports is still using an old compiler.
So does anybody know how I can fix this problem?
Also, why is macports still using gcc-4.2, while I have all my symlinks pointing at /opt/local/bin/gcc-mp-4.8. I remember having this problem earlier with installing some other python packages (or maybe it was this one, I don't remember), so I forced macports to use the newer compiler by changing the makefile and it worked temporarily. Until I started upgrading my outdated ports. Obviously now macports encountered linking errors and just reinstalled the all those packages (this is where I am now). So why does macports not just use the newer compiler? Or how can I make him do this? (maybe I shouldn't?)
Any help is appreciated. Thanks.
On 10.5.8 with Xcode 3.1.4 MacPorts uses the following compilers (in-order, unless blacklisted by ports because known to break):
GCC 4.2 from /usr/bin
A MacPorts build of the same compiler (with a few minor bugfixes)
GCC 4.0 from /usr/bin
Clang 3.3 from MacPorts
It seems this port should be blacklisting GCC 4.2 (and probably 2. and 3., too). You could file that as a bug, but to be honest, support for 10.5 is only given on a best-effort basis because most maintainers can't test on this platform anymore, so that's probably not getting you anywhere unless you provide a patch with your report.
You could override the compiler from command line like you did before. To stop rev-upgrade from immediately starting rebuilds, you can set revupgrade_mode report in your macports.conf. I'd have to see the output of port -dy rev-upgrade when it encounters broken ports to know why it produces broken binaries.
It has already been mentioned that the select mechanism doesn't affect which compilers MacPorts chooses for its ports (because depending on what's selected by the user would add another variable that might make builds unreproducible, which is something we're trying to avoid). MacPorts' default compilers can be changed, but doing so is completely unsupported and deliberately undocumented. That being said, if you still want to attempt this, https://apple.stackexchange.com/questions/118550/define-local-keyword-globally-in-a-macports-config/122997#122997 has some info on how to do that.